GLM-based optimization of NGS data analysis: A case study of Roche 454, Ion Torrent PGM and Illumina NextSeq sequencing data.

ABSTRACT:

Background

There are various next-generation sequencing techniques, all of them striving to replace Sanger sequencing as the gold standard. However, false positive calls of single nucleotide variants and especially indels are a widely known problem of basically all sequencing platforms.

Methods

We considered three common next-generation sequencers-Roche 454, Ion Torrent PGM and Illumina NextSeq-and applied standard as well as optimized variant calling pipelines. Optimization was achieved by combining information of 23 diverse parameters characterizing the reported variants and generating individually calibrated generalized linear models. Models were calibrated using amplicon-based targeted sequencing data (19 genes, 28,775 bp) from seven to 12 myelodysplastic syndrome patien

SUBMITTER: Sandmann S 

PROVIDER: S-EPMC5319672 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature